The potential of genomics for infectious disease forecasting
Genomic technologies have led to tremendous gains in understanding how pathogens
function, evolve and interact. Pathogen diversity is now measurable at high precision and …
function, evolve and interact. Pathogen diversity is now measurable at high precision and …
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires
The adaptive immune system recognizes antigens via an immense array of antigen-binding
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …
antibodies and T-cell receptors, the immune repertoire. The interrogation of immune …
A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants
The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective
vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by …
vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by …
RPANDA: an R package for macroevolutionary analyses on phylogenetic trees
A number of approaches for studying macroevolution using phylogenetic trees have been
developed in the last few years. Here, we present RPANDA, an R package that implements …
developed in the last few years. Here, we present RPANDA, an R package that implements …
Is BAMM flawed? Theoretical and practical concerns in the analysis of multi-rate diversification models
Bayesian analysis of macroevolutionary mixtures (BAMM) is a statistical framework that uses
reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of …
reversible jump Markov chain Monte Carlo to infer complex macroevolutionary dynamics of …
Microhabitat change drives diversification in pholcid spiders
J Eberle, D Dimitrov, A Valdez-Mondragón… - BMC Evolutionary …, 2018 - Springer
Background Microhabitat changes are thought to be among the main drivers of
diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we …
diversification. However, this conclusion is mostly based on studies on vertebrates. Here, we …
Connecting the Dots--Density-Connectivity Distance unifies DBSCAN, k-Center and Spectral Clustering
Despite the popularity of density-based clustering, its procedural definition makes it difficult
to analyze compared to clustering methods that minimize a loss function. In this paper, we …
to analyze compared to clustering methods that minimize a loss function. In this paper, we …
Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks
Widely applicable, accurate and fast inference methods in phylodynamics are needed to
fully profit from the richness of genetic data in uncovering the dynamics of epidemics …
fully profit from the richness of genetic data in uncovering the dynamics of epidemics …
Distance metrics for ranked evolutionary trees
J Kim, NA Rosenberg… - Proceedings of the …, 2020 - National Acad Sciences
Genealogical tree modeling is essential for estimating evolutionary parameters in population
genetics and phylogenetics. Recent mathematical results concerning ranked genealogies …
genetics and phylogenetics. Recent mathematical results concerning ranked genealogies …
Generative power of a protein language model trained on multiple sequence alignments
Computational models starting from large ensembles of evolutionarily related protein
sequences capture a representation of protein families and learn constraints associated to …
sequences capture a representation of protein families and learn constraints associated to …